Our study aimed to demonstrate the influence of left ventricular (LV) diastolic dysfunction on the diagnostic performance of coronary computed tomography angiography-derived fractional flow reserve (CT-FFR). One hundred vessels from 90 patients were retrospectively analyzed. All patients underwent echocardiography, coronary computed tomography angiography (CCTA), CT-FFR, invasive coronary angiography (ICA), and fractional flow reserve (FFR). The study population was divided into normal and dysfunction groups according to the LV diastolic function, and the diagnostic performance in both groups was assessed. There was a good correlation between CT-FFR and FFR (R = 0.768 p < 0.001) on a per-vessel basis. The sensitivity, specificity, and accuracy were 82.3%, 81.8%, and 82%, respectively. The sensitivity, specificity, and accuracy were 84.6%, 88.5%, and 87.2% in the normal group and 81%, 77.5%, and 78.7% in the dysfunction group, respectively. CT-FFR showed no statistically significant difference in the AUC in the normal group vs. the dysfunction group (AUC: 0.920 [95% CI 0.787-0.983] vs. 0.871 [95% CI 0.761-0.943], Z = 0.772 p = 0.440). However, there was still a good correlation between CT-FFR and FFR in the normal group (R = 0.767, p < 0.001) and dysfunction group (R = 0.767 p < 0.001). LV diastolic dysfunction had no effect on the diagnostic accuracy of CT-FFR. CT-FFR has good diagnostic performance in both LV diastolic dysfunction and the normal group and can be used as an effective tool for finding lesion-specific ischemia while screening for arterial disease in patients.